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0
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1 <tool id="vep" name="Vep" version="0.1.0">
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2 <requirements>
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3 <requirement type="package" version="94.5">ensembl-vep</requirement>
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4 </requirements>
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5 <command detect_errors="exit_code"><![CDATA[
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6 #if $output_options.cell_type.strip():
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7 #set $cell_type = '--cell_type ' + str( $output_options.cell_type )
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8 #else:
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9 #set $cell_type = ''
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10 #end if
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11
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12 #if str( $output_options.individual.select ) == "all":
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13 #set $individual = '--individual all'
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14 #elif str( $output_options.individual.select ) == "ind":
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15 #set $individual = '--individual ind ' + str($output_options.individual.list)
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16 #else:
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17 #set $individual = ''
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18 #end if
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19
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20 #if str( $output_options.vcf_info_field.select ) == "other":
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21 #set $vcf_info_field = '--vcf_info_field ' + str( $output_options.vcf_info_field.name )
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22 #else
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23 #set $vcf_info_field = '--vcf_info_field ' + str( $output_options.vcf_info_field.select )
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24 #end if
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25
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26 #if str( $identifier_options.synonyms.select ) == "yes":
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27 #set $synonyms = '--synonyms ' + str( $identifier_options.synonyms.file )
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28 #else
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29 #set $synonyms = ''
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30 #end if
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31
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32 #if str( $filtering_qc.transcript_filter.select ) == "yes":
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33 #set $transcript_filter = '--transcript_filter "' + str( $filtering_qc.transcript_filter.filter ) + '"'
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34 #else:
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35 #set $transcript_filter = ''
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36 #end if
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37
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38 #if str( $filtering_qc.chr.select ) == "yes":
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39 #set chr = '--chr ' + str( $filtering_qc.chr.list )
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40 #else:
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41 #set chr = ''
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42 #end if
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43
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44 #if str( $filtering_qc.pick_order.select ) == "yes":
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45 #set $pick_order = '--pick_order ' + str( $filtering_qc.pick_order.list )
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46 #else:
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47 #set $pick_order = ''
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48 #end if
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49
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50 #if str( $filtering_qc.freq.select ) == "yes":
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51 #set $freq_pop = str( $filtering_qc.freq.freq_pop )
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52 #set $freq_freq = str( $filtering_qc.freq.freq_freq )
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53 #set $freq_gt_lt = str( $filtering_qc.freq.freq_gt_lt )
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54 #set $freq_filter = str( $filtering_qc.freq.freq_filter )
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55 #set $freq = $freq_pop + ' --freq_freq ' + $freq_freq + ' ' + $freq_gt_lt + ' ' + $freq_filter
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56 #else:
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57 #set $freq = ''
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58 #end if
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59
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60 vep
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61 --format vcf
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9
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62 --vcf
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0
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63 --no_stats
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64 --dir_plugins $__tool_directory__/dir_plugins
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65 --cache
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8
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66 --dir_cache "\$VEP_CACHE_DIR"
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0
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67 --force_overwrite
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6
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68 --species ${species}
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10
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69 --cache_version 99
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9
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70 --input_file "$input"
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0
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71 --output_file "$output"
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72 $offline
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73 $output_options.variant_class
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74 $output_options.sift
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75 $output_options.polyphen
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76 $output_options.humdiv
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77 $output_options.nearest
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78 --distance $output_options.distance
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79 $output_options.gene_phenotype
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80 $output_options.regulatory
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81 $cell_type
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82 $individual
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83 $vcf_info_field
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84 $output_options.phased
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85 $output_options.total_length
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86 $output_options.numbers
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87 $output_options.domains
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88 $output_options.no_escape
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89 $output_options.keep_csq
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90 --terms $output_options.terms
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91 $output_options.no_headers
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92 $identifier_options.transcript_version
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93 $identifier_options.protein
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94 $identifier_options.symbol
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95 $identifier_options.ccds
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96 $identifier_options.tsl
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97 $identifier_options.appris
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98 $identifier_options.canonical
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99 $identifier_options.biotype
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100 $identifier_options.xref_refseq
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101 $synonyms
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102 $co_located_variants_options.check_existing
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103 $co_located_variants_options.exclude_null_alleles
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104 $co_located_variants_options.no_check_alleles
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105 $co_located_variants_options.af
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106 $co_located_variants_options.max_af
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107 $co_located_variants_options.af_1kg
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108 $co_located_variants_options.af_esp
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109 $co_located_variants_options.af_gnomad
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110 $co_located_variants_options.af_exac
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111 $co_located_variants_options.pubmed
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112 $co_located_variants_options.failed
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113 $filtering_qc.gencode_basic
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114 $filtering_qc.all_refseq
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115 $filtering_qc.exclude_predicted
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116 $transcript_filter
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117 $filtering_qc.check_ref
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118 $filtering_qc.lookup_ref
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119 $chr
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120 $filtering_qc.dont_skip
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121 $filtering_qc.allow_non_variant
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122 $filtering_qc.coding_only
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123 $filtering_qc.no_intergenic
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124 $filtering_qc.pick
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125 $filtering_qc.pick_allele
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126 $filtering_qc.pick_allele_gene
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127 $filtering_qc.per_gene
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128 $filtering_qc.flag_pick
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129 $filtering_qc.flag_pick_allele
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130 $filtering_qc.flag_pick_allele_gene
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131 $pick_order
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132 $filtering_qc.most_severe
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133 $filtering_qc.summary
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134 $filtering_qc.filter_common
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135 $freq
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136 #for $i, $s in enumerate( $other_anotations.plugins )
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137 --plugin $s.plugin
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138 #end for
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139 ]]></command>
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140 <inputs>
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141 <param type="data" name="input" format="vcf" />
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142 <param name="species" type="select">
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6
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143 <option value="mus_musculus" selected="true">Mus musculus</option>
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144 <option value="homo_sapiens">Homo sapiens</option>
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145 </param>
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146 <param name="cache_type" type="select">
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147 <option value="" selected="true">ensembl</option>
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148 <option value="--refseq">refseq</option>
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149 <option value="--merged">merged</option>
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0
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150 </param>
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151 <param name="offline" type="select">
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152 <option value="--offline">Yes</option>
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153 <option value="" selected="true">No</option>
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154 </param>
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155 <section name="output_options" title="Output options">
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156 <param name="variant_class" type="select">
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157 <option value="--variant_class">Yes</option>
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158 <option value="" selected="true">No</option>
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159 </param>
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160 <param name="sift" type="select">
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161 <option value="--sift p">Prediction</option>
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162 <option value="--sift s">Score</option>
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163 <option value="--sift b">Both</option>
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164 <option value="" selected="true">No</option>
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165 </param>
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166 <param name="polyphen" type="select">
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167 <option value="--polyphen p">Prediction</option>
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168 <option value="--polyphen s">Score</option>
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169 <option value="--polyphen b">Both</option>
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170 <option value="" selected="true">No</option>
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171 </param>
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172 <param name="humdiv" type="select">
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173 <option value="--humdiv">Yes</option>
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174 <option value="" selected="true">No</option>
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175 </param>
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176 <param name="nearest" type="select">
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177 <option value="--nearest transcript">Transcript</option>
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178 <option value="--nearest gene">Gene</option>
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179 <option value="--nearest symbol">Symbol</option>
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180 <option value="" selected="true">No</option>
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181 </param>
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182 <param name="distance" type="text" value="5000">
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183 <validator type="regex" message="Has to be a number">\d+(,\d+)?</validator>
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184 </param>
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185 <param name="gene_phenotype" type="select">
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186 <option value="--gene_phenotype">Yes</option>
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187 <option value="" selected="true">No</option>
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188 </param>
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189 <param name="regulatory" type="select">
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190 <option value="--regulatory">Yes</option>
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191 <option value="" selected="true">No</option>
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192 </param>
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193 <param name="cell_type" type="text"/>
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194 <conditional name="individual">
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195 <param name="select" type="select" label="individual">
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196 <option value="all">All</option>
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197 <option value="ind">Individual/List</option>
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198 <option value="no" selected="true">No</option>
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199 </param>
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200 <when value="ind">
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201 <param name="list" type="text" />
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202 </when>
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203 </conditional>
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204
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205 <param name="phased" type="select">
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206 <option value="--phased">Yes</option>
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207 <option value="" selected="true">No</option>
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208 </param>
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209 <param name="total_length" type="select">
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210 <option value="--total_length">Yes</option>
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211 <option value="" selected="true">No</option>
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212 </param>
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213 <param name="numbers" type="select">
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214 <option value="--numbers">Yes</option>
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215 <option value="" selected="true">No</option>
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216 </param>
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217 <param name="domains" type="select">
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218 <option value="--domains">Yes</option>
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219 <option value="" selected="true">No</option>
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220 </param>
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221 <param name="no_escape" type="select">
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222 <option value="--no_escape">Yes</option>
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223 <option value="" selected="true">No</option>
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224 </param>
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225 <param name="keep_csq" type="select">
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226 <option value="--no_escape">Yes</option>
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227 <option value="" selected="true">No</option>
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228 </param>
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229 <conditional name="vcf_info_field">
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230 <param name="select" type="select" label="vcf_info_field">
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231 <option value="CSQ" selected="true">CSQ</option>
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232 <option value="ANN">ANN</option>
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233 <option value="other">Other</option>
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234 </param>
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235 <when value="other">
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236 <param name="name" type="text" />
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237 </when>
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238 </conditional>
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239 <param name="terms" type="select">
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240 <option value="SO" selected="true">SO</option>
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241 <option value="display">display</option>
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242 <option value="NCBI">NCBI</option>
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243 </param>
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244 <param name="no_headers" type="select">
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245 <option value="--no_headers">Yes</option>
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246 <option value="" selected="true">No</option>
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247 </param>
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248 </section>
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249
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250 <section name="identifier_options" title="Identifiers options">
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251 <!-- TODO add hgvs -->
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252 <!-- TODO add hgvsg -->
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253 <!-- TODO add shift_hgvs -->
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254 <param name="transcript_version" type="select">
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255 <option value="--transcript_version">Yes</option>
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256 <option value="" selected="true">No</option>
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257 </param>
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258 <param name="protein" type="select">
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259 <option value="--protein">Yes</option>
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260 <option value="" selected="true">No</option>
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261 </param>
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262 <param name="symbol" type="select">
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263 <option value="--symbol">Yes</option>
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264 <option value="" selected="true">No</option>
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265 </param>
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266 <param name="ccds" type="select">
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267 <option value="--ccds">Yes</option>
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268 <option value="" selected="true">No</option>
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269 </param>
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270 <param name="tsl" type="select">
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271 <option value="--tsl">Yes</option>
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272 <option value="" selected="true">No</option>
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273 </param>
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274 <param name="appris" type="select">
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275 <option value="--appris">Yes</option>
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276 <option value="" selected="true">No</option>
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277 </param>
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278 <param name="canonical" type="select">
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279 <option value="--canonical">Yes</option>
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280 <option value="" selected="true">No</option>
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281 </param>
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282 <param name="biotype" type="select">
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283 <option value="--biotype">Yes</option>
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284 <option value="" selected="true">No</option>
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285 </param>
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286 <param name="xref_refseq" type="select">
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287 <option value="--xref_refseq">Yes</option>
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288 <option value="" selected="true">No</option>
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289 </param>
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290 <conditional name="synonyms">
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291 <param name="select" type="select" label="synonyms">
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292 <option value="yes">Yes</option>
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293 <option value="no" selected="true">No</option>
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294 </param>
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295 <when value="yes">
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296 <param type="data" name="file" format="tabular" />
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297 </when>
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298 </conditional>
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299 </section>
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300
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301 <section name="co_located_variants_options" title="Co-located variants options">
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302 <param name="check_existing" type="select">
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303 <option value="--check_existing">Yes</option>
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304 <option value="" selected="true">No</option>
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305 </param>
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306 <param name="exclude_null_alleles" type="select">
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307 <option value="--exclude_null_alleles">Yes</option>
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308 <option value="" selected="true">No</option>
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309 </param>
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310 <param name="no_check_alleles" type="select">
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311 <option value="--no_check_alleles">Yes</option>
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312 <option value="" selected="true">No</option>
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313 </param>
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314 <param name="af" type="select">
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315 <option value="--af">Yes</option>
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316 <option value="" selected="true">No</option>
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317 </param>
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318 <param name="max_af" type="select">
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319 <option value="--max_af">Yes</option>
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320 <option value="" selected="true">No</option>
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321 </param>
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322 <param name="af_1kg" type="select">
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323 <option value="--af_1kg">Yes</option>
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324 <option value="" selected="true">No</option>
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325 </param>
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326 <param name="af_esp" type="select">
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327 <option value="--af_esp">Yes</option>
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328 <option value="" selected="true">No</option>
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329 </param>
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330 <param name="af_gnomad" type="select">
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331 <option value="--af_gnomad">Yes</option>
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332 <option value="" selected="true">No</option>
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333 </param>
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334 <param name="af_exac" type="select">
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335 <option value="--af_exac">Yes</option>
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336 <option value="" selected="true">No</option>
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337 </param>
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338 <param name="pubmed" type="select">
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339 <option value="--pubmed">Yes</option>
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340 <option value="" selected="true">No</option>
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341 </param>
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342 <param name="failed" type="select">
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343 <option value="--failed 1">Yes</option>
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344 <option value="--failed 0" selected="true">No</option>
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345 </param>
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346 </section>
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347
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348 <section name="filtering_qc" title="Filtering and QC">
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349 <param name="gencode_basic" type="select">
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350 <option value="--gencode_basic">Yes</option>
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351 <option value="" selected="true">No</option>
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352 </param>
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353 <param name="all_refseq" type="select">
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354 <option value="--all_refseq">Yes</option>
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355 <option value="" selected="true">No</option>
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356 </param>
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357 <param name="exclude_predicted" type="select">
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358 <option value="--exclude_predicted">Yes</option>
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359 <option value="" selected="true">No</option>
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360 </param>
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361 <conditional name="transcript_filter">
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362 <param name="select" type="select" label="transcript_filter">
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363 <option value="yes">Yes</option>
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364 <option value="no" selected="true">No</option>
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365 </param>
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366 <when value="yes">
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367 <param type="text" name="filter">
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368 <sanitizer>
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369 <valid initial="string.printable">
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370 <remove value="'" />
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371 </valid>
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372 </sanitizer>
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373 </param>
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374 </when>
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375 </conditional>
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376 <param name="check_ref" type="select">
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377 <option value="--check_ref">Yes</option>
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378 <option value="" selected="true">No</option>
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379 </param>
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380 <param name="lookup_ref" type="select">
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381 <option value="--lookup_ref">Yes</option>
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382 <option value="" selected="true">No</option>
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383 </param>
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384 <conditional name="chr"> <!-- TODO double check, looks correct but doesn't seem to work -->
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385 <param name="select" type="select" label="chr">
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386 <option value="yes">Yes</option>
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387 <option value="no" selected="true">No</option>
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388 </param>
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389 <when value="yes">
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390 <param type="text" name="list" />
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391 </when>
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392 </conditional>
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393 <param name="dont_skip" type="select">
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394 <option value="" selected="true">Yes</option>
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395 <option value="--dont_skip">No</option>
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396 </param>
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397 <param name="allow_non_variant" type="select">
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398 <option value="--allow_non_variant">Yes</option>
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399 <option value="" selected="true">No</option>
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400 </param>
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401 <param name="coding_only" type="select">
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402 <option value="--coding_only">Yes</option>
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403 <option value="" selected="true">No</option>
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404 </param>
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405 <param name="no_intergenic" type="select">
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406 <option value="--no_intergenic">Yes</option>
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407 <option value="" selected="true">No</option>
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408 </param>
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409 <param name="pick" type="select">
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410 <option value="--pick">Yes</option>
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411 <option value="" selected="true">No</option>
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412 </param>
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413 <param name="pick_allele" type="select">
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414 <option value="--pick_allele">Yes</option>
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415 <option value="" selected="true">No</option>
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416 </param>
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417 <param name="pick_allele_gene" type="select">
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418 <option value="--pick_allele_gene">Yes</option>
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419 <option value="" selected="true">No</option>
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420 </param>
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421 <param name="per_gene" type="select">
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422 <option value="--per_gene">Yes</option>
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423 <option value="" selected="true">No</option>
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424 </param>
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425 <param name="flag_pick" type="select">
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426 <option value="--flag_pick">Yes</option>
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427 <option value="" selected="true">No</option>
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428 </param>
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429 <param name="flag_pick_allele" type="select">
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430 <option value="--flag_pick_allele">Yes</option>
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431 <option value="" selected="true">No</option>
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432 </param>
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433 <param name="flag_pick_allele_gene" type="select">
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434 <option value="--flag_pick_allele_gene">Yes</option>
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435 <option value="" selected="true">No</option>
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436 </param>
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437 <conditional name="pick_order">
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438 <param name="select" type="select" label="pick_order">
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439 <option value="yes">Yes</option>
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440 <option value="no" selected="true">No</option>
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441 </param>
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442 <when value="yes">
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443 <param type="text" name="list" />
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444 </when>
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445 </conditional>
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446 <param name="most_severe" type="select">
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447 <option value="--most_severe">Yes</option>
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448 <option value="" selected="true">No</option>
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449 </param>
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450 <param name="summary" type="select"> <!-- TODO double check, looks correct but doesn't seem to work -->
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451 <option value="--summary">Yes</option>
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452 <option value="" selected="true">No</option>
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453 </param>
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454 <param name="filter_common" type="select">
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455 <option value="--filter_common">Yes</option>
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456 <option value="" selected="true">No</option>
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457 </param>
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458
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459 <conditional name="freq">
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460 <param name="select" type="select" label="freq">
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461 <option value="yes">Yes</option>
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462 <option value="no" selected="true">No</option>
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463 </param>
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464 <when value="yes">
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465 <param name="freq_pop" type="select">
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466 <option value="--freq_pop 1KG_ALL">1000 genomes combined population (global)</option>
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467 <option value="--freq_pop 1KG_AFR">1000 genomes combined African population</option>
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468 <option value="--freq_pop 1KG_AMR">1000 genomes combined American population</option>
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469 <option value="--freq_pop 1KG_EAS">1000 genomes combined East Asian population</option>
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470 <option value="--freq_pop 1KG_EUR">1000 genomes combined European population</option>
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471 <option value="--freq_pop 1KG_SAS">1000 genomes combined South Asian population</option>
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472 <option value="--freq_pop ESP_AA">NHLBI-ESP African American</option>
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473 <option value="--freq_pop ESP_EA">NHLBI-ESP European American</option>
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474 <option value="--freq_pop gnomAD">gnomAD combined population</option>
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475 <option value="--freq_pop gnomAD_AFR">gnomAD African/African American population</option>
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476 <option value="--freq_pop gnomAD_AMR">gnomAD Latino population</option>
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477 <option value="--freq_pop gnomAD_ASJ">gnomAD Ashkenazi Jewish population</option>
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478 <option value="--freq_pop gnomAD_EAS">gnomAD East Asian population</option>
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479 <option value="--freq_pop gnomAD_FIN">gnomAD Finnish population</option>
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480 <option value="--freq_pop gnomAD_NFE">gnomAD non-Finnish European population</option>
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|
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481 <option value="--freq_pop gnomAD_OTH">gnomAD other population</option>
|
|
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482 <option value="--freq_pop gnomAD_SAS">gnomAD South Asian population</option>
|
|
|
483 </param>
|
|
|
484 <param type="text" name="freq_freq" />
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|
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485 <param name="freq_gt_lt" type="select">
|
|
|
486 <option value="--freq_gt_lt gt" selected="true">Greater</option>
|
|
|
487 <option value="--freq_gt_lt lt">Less than</option>
|
|
|
488 </param>
|
|
|
489 <param name="freq_filter" type="select">
|
|
|
490 <option value="--freq_filter include" selected="true">Include</option>
|
|
|
491 <option value="--freq_gt_lt exclude">Exclude</option>
|
|
|
492 </param>
|
|
|
493 </when>
|
|
|
494 </conditional>
|
|
|
495
|
|
|
496 <!-- TODO add check_frequency group -->
|
|
|
497 </section>
|
|
|
498
|
|
|
499 <section name="other_anotations" title="Other anotations">
|
|
|
500 <repeat name="plugins" title="Plugins" min="0" default="0">
|
|
|
501 <param name="plugin" type="select" label="Plugin">
|
|
|
502 <option value="AncestralAllele">AncestralAllele</option>
|
|
|
503 <option value="Blosum62">Blosum62</option>
|
|
|
504 <option value="CADD">CADD</option>
|
|
|
505 <option value="Carol">Carol</option>
|
|
|
506 <option value="CCDSFilter">CCDSFilter</option>
|
|
|
507 <option value="Condel">Condel</option>
|
|
|
508 <option value="Conservation">Conservation</option>
|
|
|
509 <option value="CSN">CSN</option>
|
|
|
510 <option value="DAS">DAS</option>
|
|
|
511 <option value="dbNSFP">dbNSFP</option>
|
|
|
512 <option value="dbscSNV">dbscSNV</option>
|
|
|
513 <option value="Downstream">Downstream</option>
|
|
|
514 <option value="Draw">Draw</option>
|
|
|
515 <option value="ExACpLI">ExACpLI</option>
|
|
|
516 <option value="ExAC">ExAC</option>
|
|
|
517 <option value="FATHMM_MKL">FATHMM_MKL</option>
|
|
|
518 <option value="FATHMM">FATHMM</option>
|
|
|
519 <option value="G2P">G2P</option>
|
|
|
520 <option value="GeneSplicer">GeneSplicer</option>
|
|
|
521 <option value="GO">GO</option>
|
|
|
522 <option value="GXA">GXA</option>
|
|
|
523 <option value="HGVSReferenceBase">HGVSReferenceBase</option>
|
|
|
524 <option value="LD">LD</option>
|
|
|
525 <option value="LocalID">LocalID</option>
|
|
|
526 <option value="LoFtool">LoFtool</option>
|
|
|
527 <option value="LOVD">LOVD</option>
|
|
|
528 <option value="MaxEntScan">MaxEntScan</option>
|
|
|
529 <option value="miRNA">miRNA</option>
|
|
|
530 <option value="MPC">MPC</option>
|
|
|
531 <option value="MTR">MTR</option>
|
|
|
532 <option value="NearestGene">NearestGene</option>
|
|
|
533 <option value="NonSynonymousFilter">NonSynonymousFilter</option>
|
|
|
534 <option value="Phenotypes">Phenotypes</option>
|
|
|
535 <option value="PolyPhen_SIFT">PolyPhen_SIFT</option>
|
|
|
536 <option value="PON_P2">PON_P2</option>
|
|
|
537 <option value="ProteinSeqs">ProteinSeqs</option>
|
|
|
538 <option value="RankFilter">RankFilter</option>
|
|
|
539 <option value="RefSeqHGVS">RefSeqHGVS</option>
|
|
|
540 <option value="REVEL">REVEL</option>
|
|
|
541 <option value="SameCodon">SameCodon</option>
|
|
|
542 <option value="SpliceRegion">SpliceRegion</option>
|
|
|
543 <option value="SubsetVCF">SubsetVCF</option>
|
|
|
544 <option value="TSSDistance">TSSDistance</option>
|
|
|
545 <option value="Wildtype">Wildtype</option>
|
|
|
546 </param>
|
|
|
547 </repeat>
|
|
|
548 </section>
|
|
|
549
|
|
|
550
|
|
|
551
|
|
|
552 </inputs>
|
|
|
553 <outputs>
|
|
|
554 <data name="output" format="vcf" />
|
|
|
555 </outputs>
|
|
|
556 <help><![CDATA[
|
|
|
557 This is a straightforward tool wrapper for VEP, for more information about these parameters visit the VEP documentation: https://www.ensembl.org/info/docs/tools/vep/script/vep_options.html
|
|
|
558 ]]></help>
|
|
5
|
559 </tool>
|
